Seen In: Superman: The Movie (1978), Man of Steel (2013)
Less a physical prison, more an 'alternate dimension,' the Phantom Zone was discovered by the Kryptonian scientist Jor-El as a solution to the society's incarceration issues. Prior to the discovery of the Zone, inmates were cryogenically frozen and launched into planetary orbit while a small device removed their brains of 'badness.'
We'll admit that using an alternate dimension in which people never age, die, eat, or sleep as basically a guard-less prison seems like a wasted opportunity, but the Zone itself is impressive. Man of Steel updated the cinematic take on the Zone by actually tearing open a portal, and swallowing a prison ship whole. Recent comics have revealed that their actually are creature who live in the Zone, and aren't too crazy about Krypton's uses - or the implication that their home is a ghostly purgatory.